I agree with Josieb1--use calibre or another conversion program. But even then don't expect great results. PDFs were never intend for reflowable text. PDFs therefore are often not converted well to any ebook format.

Since the ebook you got back is not an exact copy of the original, it has been converted. The result should always be an .azw (MOBI) file, but if Amazon can't convert the PDF to text it will instead convert it to images. This was more useful before the Kindle could read PDFs - now it is probably a waste of time.

As Josieb1 says, you might want to try Calibre's PDF to MOBI conversion. Calibre is very easy to use, and is worth installing if you expect to read any significant number of your own documents on the Kindle. However, some PDFs are just intrinsically hard to convert to another format - so don't be surprised if Calibre's conversion is also a bust.

I wonder if the original PDF was perhaps also a graphic file, such as would be created by scanning a paper article and saving the results as a pdf.

I myself had a similar experience with a graphic-based PDF. Before the conversion to Kindle format, you could at least zoom, but after using the Convert email function I could not. It did not much matter, because it was too frustrating to read either way.

Fortunately, the great majority of pdf's on the web are not based on scanned images.

If you really want it converted cleanly, try Calibre's debug mode (click convert, then scroll down to the cute little lady bug in the left pane). A lot of times, you can fix the major problems by editing the html output in one of the debug folders. Calibre outputs four versions: Input, Parsed, Processed, and Structure. So, you can pick which version looks best and tweak from there (I'd start with Parsed, and go back to Input if necessary).

If Calibre extracts nothing but jpegs, you can still work with that. Use Mobipocket Creator to create a new book and add the images (in correct order) to the Publication Files (I'm not in front of Windows right now, so I'm relying on memory - if it's not called "Publication Files" it's something similar).